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ananyo writes "Proteins are an enormous molecular achievement: chains of amino acids that fold spontaneously into a precise conformation, time after time, optimized by evolution for their particular function. Yet given the exponential number of contortions possible for any chain of amino acids, dictating a sequence that will fold into a predictable structure has been a daunting task. Now researchers report that they can do just that. By following a set of rules described in a paper published in Nature (abstract), a husband and wife team from David Baker's laboratory at the University of Washington in Seattle has designed five proteins from scratch that fold reliably into predicted conformations. The work could eventually allow scientists to custom design proteins with specific functions."

By following a set of rules described in a paper published in Nature (abstract), a husband and wife team from David Baker's laboratory at the University of Washington in Seattle has designed five proteins from scratch that fold reliably into predicted conformations.

Barring certain genetic anomalies, it should be pretty easy for any husband and wife team to produce protein sequences that result in predicted conformations.

Because, unless your're His Noodliness, you have to start out small. We can make DNA of reasonable length but we don't know how to create a sequence that will cause a protein to fold in a specific pattern to it will have a specific function and not act like a disorganized blob of glop.

You want to be the whole spaghetti, not just the stuff tossed out in the sink.

Now we're invited to celebrate the achievement/intelligence of these ones who managed to fold a simple protein that would have folded itself into something far complex and useful, given enough time to "evolve"? Am I the only one who sees the vanity in this reasoning?

What vanity is there in doing it right in the first try? It is a very interesting achievement, one that relies not on the blind luck of evolution but on the application of a limited set of rules.

If evoultion worked like this, perhaps our retinas wouldn't be turned inside out as the currently are (for example).

How about we stay quiet until we can create a living thing from scratch that's more impressive than the life-forms the random unintelligent process of evolution has come up with.

Impressive is a subjective quality: while you may only find a whale-size elephant impressive, I find it quite impressive that someone has managed to do from scratch what evolution might only do after

What would you call a retina that has the photoreceptors hidden behind the axons and the blood vessels so the blood vessels and the axons are inside the sphere area corresponding to the photoreceptors? Compare it to the octopus eye which has no extra layers between the light and the photoreceptors.

...are flawed and could be better designed - isn't what's "right" or "correct" here also subjective by your own argument?

They are flawed since they could be much more efficient "just" by having the layers in the right order, as in cephalopods. It just happens that evolution didn't have a plan at all (that's what evolution does, an

Mark my words, it's only a matter of time before someone discovers that what were previously thought to be imperfections in the design of the eyes of vertebrates actually make it far superior to the octopus eye...

Excuse me if I don't hold my breath. I'm not an octopus, mind you;)

I respect science and research but some of this stuff is just the opinion of arrogant men who are obsessed with their own ideas of how things should be (i.e. they are delusional). Remember Fred Hoyle?

What would you need to not consider it "just the opinion of arrogant men"? Actually, I think that considering the human/mammal eye to be suboptimal shows more humbleness than arrogance, at least if you consider the millennia during which humans have asserted their being at the cusp of everything. And then it was discovered that the Earth wasn't the center of the solar system, that the solar system wasn't the center of the universe... I real

This is actually a fairly important discovery. The poster of the article seems to be completely clueless as to why it is important.

Without going into all of the details, being able to predict the shape of proteins is one of the things needed to make nanotechnology fulfill its potential - to build a nanotech "assembler".

If you want all the details you would have to go back to "Engines of Creation" by Eric Drexler.

Proteins of the right shape can be used to create complex structures - anything from a virus to a nano-computer. Construct some RNA, feed it into a cell and get back as many copies of the protein chain as you please.

Do this for several different proteins.

Leave all of these proteins in the same chemical soup and they will combine on their own to form the more complex structuresl

But if you can't predict the shape the protein folds into, you can't get started. This has been a key problem in nano-tech going back to the 1970s.

If this happens this could open up a new era in medicine.It is literally *the* cure for hiv , cancer and just about everything else. Specific proteins can be created to attach to and kill exactly just about anything , it's the perfect artificial immune system.The gloomy side of this is that it will also open up the door for new weapons. One could theoretically build proteins designed to kill exactly one individual potentially without leaving much of a trace to the untrained eye.

I've always said that protein engineering will become more important to humanity than the transistor, For just one example of the incredible potential proteins have, look at enzymes. These are biological catalysts that tirelessly perform very specific chemical reactions. In the case of some enzymes, they are called 'kinetically perfect', meaning that they are so fast the only way we have of explaining the reaction speed is that every time the molecule they work on collides with the enzyme, the reaction immediately happens. Mind-blowingly, some enzymes are even faster than this, so-called 'better than kinetically perfect' and how they manage their astounding speed is one of biology's great unsolved problems.

Some other cool example of proteins: Proton pumps in your stomach, which carry individual protons into your stomach to make acid. Photosystems 1 and 2 in plant chloroplasts, which juggle electrons between each other and weave sunlight into sugar, forming the basis of the whole earth's food chain.

Photosynthesis is achieved by having a very specialized enzyme that works like a workshop bench. It clamps down the hydrogen bonds of the H2O molecule and literally snips off the hydrogen atoms using the energy from several UV photons. All done using the electrical charges of chemical bonds and free electrons.

In the case of some enzymes, they are called 'kinetically perfect', meaning that they are so fast the only way we have of explaining the reaction speed is that every time the molecule they work on collides with the enzyme, the reaction immediately happens. Mind-blowingly, some enzymes are even faster than this

So... thiotimoline is an enzyme? Biochemist Dr. Asimov was wrong about its composition?

I remember hearing that DNA polymerase runs so fast along DNA that if it were a train, and the base pairs were railroad ties, it would be moving something like a thousand miles an hour. And it would be duplicating the train tracks nearly perfectly as it did so.

The other day I reflected over the lack of knowing how these foldings work; I recalled some tv program for the 70s that had identified this as a big issue back then Voila, today we have a working progress.

I used to work in a protein engineering lab that collaborated extensively with Baker's lab. Let me be the first to say the quality of work coming out of there is outstanding. Protein engineering is incredibly difficult and their Rosetta software (protein folding again) is pretty much essential (yeah yeah, there's other software and rosetta has flaws, like not taking charged amino acids into account, but really its the best we have) -- even more so than pymol for any design you'd be doing.

This is the second large break through coming from them in the past few years. The other one was designing enzyme that performed a totally novel reaction. Details here: http://www.sciencemag.org/content/329/5989/309 . I really can't stress how big of a deal this is for designed (chemical) molecules. Even if the reaction wouldn't have happened under normal conditions or without causing decomposition to the rest of the molecule, you can make an enzyme that will do it for you.

This study should help the creation process, generally directed design runs into a lot of problems with proteins that no longer fold. Being able to determine computationally what has a chance of working would greatly speed up the process. Beyond that congrats to the lab and one of the most hands on, in the science PIs I know

This is awfully cool!According to the article, they used Rosetta@home for some predictions. I wonder if they've also tried fold.it [fold.it], especially since that project is also out of U of Washington.